@jbrowse/plugin-data-management 3.1.0 → 3.3.0

package/dist/AddTrackWidget/components/PasteConfigWorkflow.js

@@ -33,12 +33,12 @@ const PasteConfigAddTrackWorkflow = (0, mobx_react_1.observer)(function ({ model
                         if ((0, util_1.isSessionWithAddTracks)(session) &&
                             (0, util_1.isSessionModelWithWidgets)(session)) {
                             (0, mobx_1.transaction)(() => {
-                                confs.forEach(c => {
+                                for (const c of confs) {
                                     session.addTrackConf(c);
-                                });
-                                confs.forEach(c => {
+                                }
+                                for (const c of confs) {
                                     model.view.showTrack(c.trackId);
-                                });
+                                }
                                 model.clearData();
                             });
                             session.hideWidget(model);

package/dist/AssemblyManager/AssemblyTable.js

@@ -5,6 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const jsx_runtime_1 = require("react/jsx-runtime");
 const configuration_1 = require("@jbrowse/core/configuration");
+const DataGridFlexContainer_1 = __importDefault(require("@jbrowse/core/ui/DataGridFlexContainer"));
 const Add_1 = __importDefault(require("@mui/icons-material/Add"));
 const Create_1 = __importDefault(require("@mui/icons-material/Create"));
 const Delete_1 = __importDefault(require("@mui/icons-material/Delete"));
@@ -12,7 +13,7 @@ const material_1 = require("@mui/material");
 const x_data_grid_1 = require("@mui/x-data-grid");
 const mobx_react_1 = require("mobx-react");
 const AssemblyTable = (0, mobx_react_1.observer)(function ({ onEditAssembly, onAddAssembly, onClose, session, }) {
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.DialogContent, { children: (0, jsx_runtime_1.jsx)("div", { style: { display: 'flex', flexDirection: 'column' }, children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rowHeight: 25, columnHeaderHeight: 35, hideFooter: session.assemblies.length < 25, rows: session.assemblies.map(assembly => ({
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.DialogContent, { children: (0, jsx_runtime_1.jsx)(DataGridFlexContainer_1.default, { children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rowHeight: 25, columnHeaderHeight: 35, hideFooter: session.assemblies.length < 25, rows: session.assemblies.map(assembly => ({
                             id: (0, configuration_1.readConfObject)(assembly, 'name'),
                             name: (0, configuration_1.readConfObject)(assembly, 'name'),
                             displayName: (0, configuration_1.readConfObject)(assembly, 'displayName'),

package/dist/HierarchicalTrackSelectorWidget/components/ShoppingCart.d.ts

@@ -1,5 +1,8 @@
-import type { HierarchicalTrackSelectorModel } from '../model';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 declare const ShoppingCart: ({ model, }: {
-    model: HierarchicalTrackSelectorModel;
+    model: {
+        clearSelection: () => void;
+        selection: AnyConfigurationModel[];
+    };
 }) => import("react/jsx-runtime").JSX.Element | null;
 export default ShoppingCart;

package/dist/HierarchicalTrackSelectorWidget/components/ShoppingCart.js

@@ -29,7 +29,10 @@ const ShoppingCart = (0, mobx_react_1.observer)(function ({ model, }) {
                     {
                         label: 'Delete tracks',
                         onClick: () => {
-                            selection.forEach(s => { var _a; return (_a = session.deleteTrackConf) === null || _a === void 0 ? void 0 : _a.call(session, s); });
+                            var _a;
+                            for (const s of selection) {
+                                (_a = session.deleteTrackConf) === null || _a === void 0 ? void 0 : _a.call(session, s);
+                            }
                         },
                     },
                 ]

package/dist/HierarchicalTrackSelectorWidget/components/faceted/FacetedDataGrid.d.ts

@@ -1,9 +1,9 @@
 import type { HierarchicalTrackSelectorModel } from '../../model';
-import type { GridColDef } from '@mui/x-data-grid';
+import type { GridColDef, GridRowId } from '@mui/x-data-grid';
 declare const FacetedDataGrid: ({ model, columns, shownTrackIds, selection, }: {
     model: HierarchicalTrackSelectorModel;
     columns: GridColDef[];
-    shownTrackIds: Set<string>;
+    shownTrackIds: Set<GridRowId>;
     selection: any[];
 }) => import("react/jsx-runtime").JSX.Element;
 export default FacetedDataGrid;

package/dist/HierarchicalTrackSelectorWidget/components/faceted/FacetedDataGrid.js

@@ -12,33 +12,42 @@ const FacetedDataGrid = (0, mobx_react_1.observer)(function ({ model, columns, s
     const { view, faceted } = model;
     const { rows, useShoppingCart, showOptions, filteredRows, filteredNonMetadataKeys, filteredMetadataKeys, visible, } = faceted;
     const [widths, setWidths] = (0, react_1.useState)({
-        name: (0, util_1.measureGridWidth)(rows.map(r => r.name), { maxWidth: 500, stripHTML: true }) + 15,
+        name: (0, util_1.measureGridWidth)(rows.map(r => r.name), {
+            maxWidth: 500,
+            stripHTML: true,
+        }) + 15,
         ...Object.fromEntries(filteredNonMetadataKeys
             .filter(f => visible[f])
             .map(e => [
             e,
-            (0, util_1.measureGridWidth)(rows.map(r => r[e]), { maxWidth: 400, stripHTML: true }),
+            (0, util_1.measureGridWidth)(rows.map(r => r[e]), {
+                maxWidth: 400,
+                stripHTML: true,
+            }),
         ])),
         ...Object.fromEntries(filteredMetadataKeys
             .filter(f => visible[`metadata.${f}`])
             .map(e => {
             return [
                 `metadata.${e}`,
-                (0, util_1.measureGridWidth)(rows.map(r => r.metadata[e]), { maxWidth: 400, stripHTML: true }),
+                (0, util_1.measureGridWidth)(rows.map(r => r.metadata[e]), {
+                    maxWidth: 400,
+                    stripHTML: true,
+                }),
             ];
         })),
     });
-    return ((0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rows: filteredRows, onColumnWidthChange: arg => {
+    return ((0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rowHeight: 25, columnHeaderHeight: 35, checkboxSelection: true, keepNonExistentRowsSelected: true, rows: filteredRows, columnVisibilityModel: visible, showToolbar: showOptions, onColumnWidthChange: arg => {
             setWidths({
                 ...widths,
                 [arg.colDef.field]: arg.width,
             });
-        }, columnVisibilityModel: visible, onColumnVisibilityModelChange: n => {
+        }, onColumnVisibilityModelChange: n => {
             model.faceted.setVisible(n);
-        }, columnHeaderHeight: 35, checkboxSelection: true, disableRowSelectionOnClick: true, keepNonExistentRowsSelected: true, onRowSelectionModelChange: userSelectedIds => {
+        }, onRowSelectionModelChange: userSelectedIds => {
             if (!useShoppingCart) {
                 const a1 = shownTrackIds;
-                const a2 = new Set(userSelectedIds);
+                const a2 = userSelectedIds.ids;
                 (0, mobx_1.transaction)(() => {
                     ;
                     [...a1].filter(x => !a2.has(x)).map(t => view.hideTrack(t));
@@ -53,19 +62,14 @@ const FacetedDataGrid = (0, mobx_react_1.observer)(function ({ model, columns, s
             else {
                 const root = (0, mobx_state_tree_1.getRoot)(model);
                 const schema = pluginManager.pluggableConfigSchemaType('track');
-                model.setSelection(userSelectedIds.map(id => (0, mobx_state_tree_1.resolveIdentifier)(schema, root, id)));
+                model.setSelection([...userSelectedIds.ids].map(id => (0, mobx_state_tree_1.resolveIdentifier)(schema, root, id)));
             }
-        }, rowSelectionModel: useShoppingCart ? selection.map(s => s.trackId) : [...shownTrackIds], slots: {
-            toolbar: showOptions ? x_data_grid_1.GridToolbar : null,
-        }, slotProps: {
-            toolbar: {
-                printOptions: {
-                    disableToolbarButton: true,
-                },
-            },
+        }, rowSelectionModel: {
+            type: 'include',
+            ids: new Set(useShoppingCart ? selection.map(s => s.trackId) : [...shownTrackIds]),
         }, columns: columns.map(r => ({
             ...r,
             width: widths[r.field],
-        })), rowHeight: 25 }));
+        })) }));
 });
 exports.default = FacetedDataGrid;

package/dist/HierarchicalTrackSelectorWidget/components/faceted/FacetedHeader.js

@@ -15,7 +15,7 @@ function FacetedHeader({ model, }) {
     const { faceted } = model;
     const [anchorEl, setAnchorEl] = (0, react_1.useState)(null);
     const { showOptions, showFilters, showSparse, useShoppingCart } = faceted;
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.Grid2, { container: true, spacing: 4, alignItems: "center", children: [(0, jsx_runtime_1.jsx)(material_1.TextField, { label: "Search...", value: faceted.filterText, onChange: event => {
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.Grid, { container: true, spacing: 4, alignItems: "center", children: [(0, jsx_runtime_1.jsx)(material_1.TextField, { label: "Search...", value: faceted.filterText, onChange: event => {
                             faceted.setFilterText(event.target.value);
                         }, slotProps: {
                             input: {

package/dist/HierarchicalTrackSelectorWidget/model.d.ts

@@ -1,5 +1,6 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { GridRowId } from '@mui/x-data-grid';
 import type { Instance } from 'mobx-state-tree';
 type MaybeAnyConfigurationModel = AnyConfigurationModel | undefined;
 type MaybeBoolean = boolean | undefined;
@@ -87,7 +88,7 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
     favorites: string[];
-    recentlyUsed: string[];
+    recentlyUsed: GridRowId[];
     selection: AnyConfigurationModel[];
     sortTrackNames: MaybeBoolean;
     sortCategories: MaybeBoolean;
@@ -109,7 +110,7 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>>;
     readonly favoritesSet: Set<string>;
-    readonly recentlyUsedSet: Set<string>;
+    readonly recentlyUsedSet: Set<GridRowId>;
     readonly assemblyNames: string[];
 } & {
     setSortTrackNames(val: boolean): void;
@@ -125,7 +126,7 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     setRecentlyUsed(str: string[]): void;
     setFavorites(str: string[]): void;
     setFavoritesCounter(val: number): void;
-    addToRecentlyUsed(id: string): void;
+    addToRecentlyUsed(id: GridRowId): void;
     clearRecentlyUsed(): void;
     setView(view: unknown): void;
     toggleCategory(pathName: string): void;

package/dist/UCSCTrackHub/configSchema.js

@@ -19,5 +19,16 @@ const UCSCTrackHubConnection = (0, configuration_1.ConfigurationSchema)('UCSCTra
     },
 }, {
     baseConfiguration: models_1.baseConnectionConfig,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                hubTxtLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
 });
 exports.default = UCSCTrackHubConnection;

package/dist/UCSCTrackHub/doConnect.js

@@ -49,6 +49,16 @@ async function doConnect(self) {
                             },
                         },
                     },
+                    ...(genome.data.chromAliasBb
+                        ? {
+                            refNameAliases: {
+                                adapter: {
+                                    type: 'BigBedAdapter',
+                                    uri: (0, util_2.resolve)(genome.data.chromAliasBb, hubUri),
+                                },
+                            },
+                        }
+                        : {}),
                 });
             }
             const asm2 = assemblyManager.get(genomeName);

package/esm/AddTrackWidget/components/PasteConfigWorkflow.js

@@ -31,12 +31,12 @@ const PasteConfigAddTrackWorkflow = observer(function ({ model, }) {
                         if (isSessionWithAddTracks(session) &&
                             isSessionModelWithWidgets(session)) {
                             transaction(() => {
-                                confs.forEach(c => {
+                                for (const c of confs) {
                                     session.addTrackConf(c);
-                                });
-                                confs.forEach(c => {
+                                }
+                                for (const c of confs) {
                                     model.view.showTrack(c.trackId);
-                                });
+                                }
                                 model.clearData();
                             });
                             session.hideWidget(model);

package/esm/AssemblyManager/AssemblyTable.js

@@ -1,5 +1,6 @@
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { readConfObject } from '@jbrowse/core/configuration';
+import DataGridFlexContainer from '@jbrowse/core/ui/DataGridFlexContainer';
 import AddIcon from '@mui/icons-material/Add';
 import CreateIcon from '@mui/icons-material/Create';
 import DeleteIcon from '@mui/icons-material/Delete';
@@ -7,7 +8,7 @@ import { Button, DialogActions, DialogContent, IconButton } from '@mui/material'
 import { DataGrid } from '@mui/x-data-grid';
 import { observer } from 'mobx-react';
 const AssemblyTable = observer(function ({ onEditAssembly, onAddAssembly, onClose, session, }) {
-    return (_jsxs(_Fragment, { children: [_jsx(DialogContent, { children: _jsx("div", { style: { display: 'flex', flexDirection: 'column' }, children: _jsx(DataGrid, { rowHeight: 25, columnHeaderHeight: 35, hideFooter: session.assemblies.length < 25, rows: session.assemblies.map(assembly => ({
+    return (_jsxs(_Fragment, { children: [_jsx(DialogContent, { children: _jsx(DataGridFlexContainer, { children: _jsx(DataGrid, { rowHeight: 25, columnHeaderHeight: 35, hideFooter: session.assemblies.length < 25, rows: session.assemblies.map(assembly => ({
                             id: readConfObject(assembly, 'name'),
                             name: readConfObject(assembly, 'name'),
                             displayName: readConfObject(assembly, 'displayName'),

package/esm/HierarchicalTrackSelectorWidget/components/ShoppingCart.d.ts

@@ -1,5 +1,8 @@
-import type { HierarchicalTrackSelectorModel } from '../model';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 declare const ShoppingCart: ({ model, }: {
-    model: HierarchicalTrackSelectorModel;
+    model: {
+        clearSelection: () => void;
+        selection: AnyConfigurationModel[];
+    };
 }) => import("react/jsx-runtime").JSX.Element | null;
 export default ShoppingCart;

package/esm/HierarchicalTrackSelectorWidget/components/ShoppingCart.js

@@ -24,7 +24,10 @@ const ShoppingCart = observer(function ({ model, }) {
                     {
                         label: 'Delete tracks',
                         onClick: () => {
-                            selection.forEach(s => { var _a; return (_a = session.deleteTrackConf) === null || _a === void 0 ? void 0 : _a.call(session, s); });
+                            var _a;
+                            for (const s of selection) {
+                                (_a = session.deleteTrackConf) === null || _a === void 0 ? void 0 : _a.call(session, s);
+                            }
                         },
                     },
                 ]

package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedDataGrid.d.ts

@@ -1,9 +1,9 @@
 import type { HierarchicalTrackSelectorModel } from '../../model';
-import type { GridColDef } from '@mui/x-data-grid';
+import type { GridColDef, GridRowId } from '@mui/x-data-grid';
 declare const FacetedDataGrid: ({ model, columns, shownTrackIds, selection, }: {
     model: HierarchicalTrackSelectorModel;
     columns: GridColDef[];
-    shownTrackIds: Set<string>;
+    shownTrackIds: Set<GridRowId>;
     selection: any[];
 }) => import("react/jsx-runtime").JSX.Element;
 export default FacetedDataGrid;

package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedDataGrid.js

@@ -1,7 +1,7 @@
 import { jsx as _jsx } from "react/jsx-runtime";
 import { useState } from 'react';
 import { getEnv, measureGridWidth } from '@jbrowse/core/util';
-import { DataGrid, GridToolbar } from '@mui/x-data-grid';
+import { DataGrid } from '@mui/x-data-grid';
 import { transaction } from 'mobx';
 import { observer } from 'mobx-react';
 import { getRoot, resolveIdentifier } from 'mobx-state-tree';
@@ -10,33 +10,42 @@ const FacetedDataGrid = observer(function ({ model, columns, shownTrackIds, sele
     const { view, faceted } = model;
     const { rows, useShoppingCart, showOptions, filteredRows, filteredNonMetadataKeys, filteredMetadataKeys, visible, } = faceted;
     const [widths, setWidths] = useState({
-        name: measureGridWidth(rows.map(r => r.name), { maxWidth: 500, stripHTML: true }) + 15,
+        name: measureGridWidth(rows.map(r => r.name), {
+            maxWidth: 500,
+            stripHTML: true,
+        }) + 15,
         ...Object.fromEntries(filteredNonMetadataKeys
             .filter(f => visible[f])
             .map(e => [
             e,
-            measureGridWidth(rows.map(r => r[e]), { maxWidth: 400, stripHTML: true }),
+            measureGridWidth(rows.map(r => r[e]), {
+                maxWidth: 400,
+                stripHTML: true,
+            }),
         ])),
         ...Object.fromEntries(filteredMetadataKeys
             .filter(f => visible[`metadata.${f}`])
             .map(e => {
             return [
                 `metadata.${e}`,
-                measureGridWidth(rows.map(r => r.metadata[e]), { maxWidth: 400, stripHTML: true }),
+                measureGridWidth(rows.map(r => r.metadata[e]), {
+                    maxWidth: 400,
+                    stripHTML: true,
+                }),
             ];
         })),
     });
-    return (_jsx(DataGrid, { rows: filteredRows, onColumnWidthChange: arg => {
+    return (_jsx(DataGrid, { rowHeight: 25, columnHeaderHeight: 35, checkboxSelection: true, keepNonExistentRowsSelected: true, rows: filteredRows, columnVisibilityModel: visible, showToolbar: showOptions, onColumnWidthChange: arg => {
             setWidths({
                 ...widths,
                 [arg.colDef.field]: arg.width,
             });
-        }, columnVisibilityModel: visible, onColumnVisibilityModelChange: n => {
+        }, onColumnVisibilityModelChange: n => {
             model.faceted.setVisible(n);
-        }, columnHeaderHeight: 35, checkboxSelection: true, disableRowSelectionOnClick: true, keepNonExistentRowsSelected: true, onRowSelectionModelChange: userSelectedIds => {
+        }, onRowSelectionModelChange: userSelectedIds => {
             if (!useShoppingCart) {
                 const a1 = shownTrackIds;
-                const a2 = new Set(userSelectedIds);
+                const a2 = userSelectedIds.ids;
                 transaction(() => {
                     ;
                     [...a1].filter(x => !a2.has(x)).map(t => view.hideTrack(t));
@@ -51,19 +60,14 @@ const FacetedDataGrid = observer(function ({ model, columns, shownTrackIds, sele
             else {
                 const root = getRoot(model);
                 const schema = pluginManager.pluggableConfigSchemaType('track');
-                model.setSelection(userSelectedIds.map(id => resolveIdentifier(schema, root, id)));
+                model.setSelection([...userSelectedIds.ids].map(id => resolveIdentifier(schema, root, id)));
             }
-        }, rowSelectionModel: useShoppingCart ? selection.map(s => s.trackId) : [...shownTrackIds], slots: {
-            toolbar: showOptions ? GridToolbar : null,
-        }, slotProps: {
-            toolbar: {
-                printOptions: {
-                    disableToolbarButton: true,
-                },
-            },
+        }, rowSelectionModel: {
+            type: 'include',
+            ids: new Set(useShoppingCart ? selection.map(s => s.trackId) : [...shownTrackIds]),
         }, columns: columns.map(r => ({
             ...r,
             width: widths[r.field],
-        })), rowHeight: 25 }));
+        })) }));
 });
 export default FacetedDataGrid;

package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedHeader.js

@@ -3,13 +3,13 @@ import { useState } from 'react';
 import { Menu } from '@jbrowse/core/ui';
 import ClearIcon from '@mui/icons-material/Clear';
 import MoreVert from '@mui/icons-material/MoreVert';
-import { Grid2, IconButton, InputAdornment, TextField } from '@mui/material';
+import { Grid, IconButton, InputAdornment, TextField } from '@mui/material';
 import ShoppingCart from '../ShoppingCart';
 export default function FacetedHeader({ model, }) {
     const { faceted } = model;
     const [anchorEl, setAnchorEl] = useState(null);
     const { showOptions, showFilters, showSparse, useShoppingCart } = faceted;
-    return (_jsxs(_Fragment, { children: [_jsxs(Grid2, { container: true, spacing: 4, alignItems: "center", children: [_jsx(TextField, { label: "Search...", value: faceted.filterText, onChange: event => {
+    return (_jsxs(_Fragment, { children: [_jsxs(Grid, { container: true, spacing: 4, alignItems: "center", children: [_jsx(TextField, { label: "Search...", value: faceted.filterText, onChange: event => {
                             faceted.setFilterText(event.target.value);
                         }, slotProps: {
                             input: {

package/esm/HierarchicalTrackSelectorWidget/model.d.ts

@@ -1,5 +1,6 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { GridRowId } from '@mui/x-data-grid';
 import type { Instance } from 'mobx-state-tree';
 type MaybeAnyConfigurationModel = AnyConfigurationModel | undefined;
 type MaybeBoolean = boolean | undefined;
@@ -87,7 +88,7 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
     favorites: string[];
-    recentlyUsed: string[];
+    recentlyUsed: GridRowId[];
     selection: AnyConfigurationModel[];
     sortTrackNames: MaybeBoolean;
     sortCategories: MaybeBoolean;
@@ -109,7 +110,7 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>>;
     readonly favoritesSet: Set<string>;
-    readonly recentlyUsedSet: Set<string>;
+    readonly recentlyUsedSet: Set<GridRowId>;
     readonly assemblyNames: string[];
 } & {
     setSortTrackNames(val: boolean): void;
@@ -125,7 +126,7 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     setRecentlyUsed(str: string[]): void;
     setFavorites(str: string[]): void;
     setFavoritesCounter(val: number): void;
-    addToRecentlyUsed(id: string): void;
+    addToRecentlyUsed(id: GridRowId): void;
     clearRecentlyUsed(): void;
     setView(view: unknown): void;
     toggleCategory(pathName: string): void;

package/esm/UCSCTrackHub/configSchema.js

@@ -17,5 +17,16 @@ const UCSCTrackHubConnection = ConfigurationSchema('UCSCTrackHubConnection', {
     },
 }, {
     baseConfiguration: baseConnectionConfig,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                hubTxtLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
 });
 export default UCSCTrackHubConnection;

package/esm/UCSCTrackHub/doConnect.js

@@ -46,6 +46,16 @@ export async function doConnect(self) {
                             },
                         },
                     },
+                    ...(genome.data.chromAliasBb
+                        ? {
+                            refNameAliases: {
+                                adapter: {
+                                    type: 'BigBedAdapter',
+                                    uri: resolve(genome.data.chromAliasBb, hubUri),
+                                },
+                            },
+                        }
+                        : {}),
                 });
             }
             const asm2 = assemblyManager.get(genomeName);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "3.1.0",
+  "version": "3.3.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -37,17 +37,17 @@
   },
   "dependencies": {
     "@gmod/ucsc-hub": "^1.0.0",
-    "@jbrowse/core": "^3.1.0",
-    "@jbrowse/plugin-config": "^3.1.0",
-    "@jbrowse/product-core": "^3.1.0",
-    "@mui/icons-material": "^6.0.0",
-    "@mui/material": "^6.0.0",
-    "@mui/x-data-grid": "^7.0.0",
+    "@jbrowse/core": "^3.3.0",
+    "@jbrowse/plugin-config": "^3.3.0",
+    "@jbrowse/product-core": "^3.3.0",
+    "@mui/icons-material": "^7.0.0",
+    "@mui/material": "^7.0.0",
+    "@mui/x-data-grid": "^8.0.0",
     "deepmerge": "^4.3.1",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
-    "react-virtualized-auto-sizer": "^1.0.2",
+    "react-virtualized-auto-sizer": "^1.0.26",
     "react-vtree": "^3.0.0-beta.1",
     "react-window": "^1.8.6",
     "tss-react": "^4.0.0"
@@ -61,5 +61,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
+  "gitHead": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
 }